LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-583-g5868aa095d-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower

read_data tiny_nylon.data   extra/bond/per/atom 5    extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 1 by 1 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  44 atoms
  reading velocities ...
  44 velocities
  scanning bonds ...
  9 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  29 = max dihedrals/atom
  scanning impropers ...
  29 = max impropers/atom
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  42 bonds
  reading angles ...
  74 angles
  reading dihedrals ...
  100 dihedrals
  reading impropers ...
  16 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        1       
  special bond factors coul:  0        0        1       
     4 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    35 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.005 seconds

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.json
Read molecule template mol1:
(no title)
  1 molecules
  0 fragments
  18 atoms with max type 0
  16 bonds with max type 8
  25 angles with max type 25
  23 dihedrals with max type 33
  2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.json
Read molecule template mol2:
(no title)
  1 molecules
  0 fragments
  18 atoms with max type 0
  17 bonds with max type 11
  31 angles with max type 24
  39 dihedrals with max type 30
  0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.json
Read molecule template mol3:
(no title)
  1 molecules
  0 fragments
  15 atoms with max type 0
  14 bonds with max type 11
  25 angles with max type 24
  30 dihedrals with max type 30
  0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.json
Read molecule template mol4:
(no title)
  1 molecules
  0 fragments
  15 atoms with max type 0
  13 bonds with max type 13
  19 angles with max type 26
  16 dihedrals with max type 29
  2 impropers with max type 5

thermo 50

# dump 1 all xyz 1 test_vis.xyz
# dump_modify 1 types labels

fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp 300 300 100

# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density f_myrxns[*]

# restart 100 restart1 restart2

run 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419

@Article{Gissinger24,
 author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
 title = {Type Label Framework for Bonded Force Fields in LAMMPS},
 journal = {J. Phys. Chem. B},
 year =    2024,
 volume =  128,
 number =  13,
 pages =   {3282--3297}
}

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287

@Article{Gissinger17,
 author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
 title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
 journal = {Polymer},
 year =    2017,
 volume =  128,
 pages =   {211--217}
}

@Article{Gissinger20,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
 journal = {Macromolecules},
 year =    2020,
 volume =  53,
 number =  22,
 pages =   {9953--9961}
}

@Article{Gissinger24,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {Molecular Modeling of Reactive Systems with REACTER},
 journal = {Computer Physics Communications},
 year =    2024,
 volume =  304,
 number =  109287
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.23408048
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.018627396
  estimated relative force accuracy = 5.6095851e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 8000 3375
Generated 55 of 55 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 10 10 10
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 34 | 34 | 34 Mbytes
   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
         0   300            357.25588      0.0034851739   0              0            
        50   328.952       -39.291672      0.0034851739   1              0            
       100   311.59495      29.741131      0.0034851739   1              1            
       150   325.04965     -19.624049      0.0034851739   1              1            
       200   313.15254      15.730975      0.0034851739   1              1            
       250   307.88805     -22.944869      0.0034851739   1              1            
       300   287.9343       6.7916738      0.0034851739   1              1            
       350   314.40601      12.913246      0.0034851739   1              1            
       400   304.58587      6.9804459      0.0034851739   1              1            
       450   300.97668      14.68689       0.0034851739   1              1            
       500   345.19498     -29.961085      0.0034851739   1              1            
       550   229.37329      12.88087       0.0034851739   1              1            
       600   239.75504     -3.575567       0.0034851739   1              1            
       650   257.58951     -5.0844118      0.0034851739   1              1            
       700   249.84121      22.825491      0.0034851739   1              1            
       750   287.62022      28.059197      0.0034851739   1              1            
       800   352.31339     -50.233738      0.0034851739   1              1            
       850   316.12821      22.493396      0.0034851739   1              1            
       900   283.85252      26.129698      0.0034851739   1              1            
       950   290.30591     -25.743121      0.0034851739   1              1            
      1000   346.57856     -2.1188627      0.0034851739   1              1            
      1050   251.23391      20.636107      0.0034851739   1              1            
      1100   267.48303     -15.912571      0.0034851739   1              1            
      1150   282.66256      14.019753      0.0034851739   1              1            
      1200   227.56518     -27.076623      0.0034851739   1              1            
      1250   232.7204      -1.0387593      0.0034851739   1              1            
      1300   277.28783      32.449571      0.0034851739   1              1            
      1350   308.5732      -11.129035      0.0034851739   1              1            
      1400   264.96641     -20.93416       0.0034851739   1              1            
      1450   262.83931      30.82366       0.0034851739   1              1            
      1500   276.23182     -24.480049      0.0034851739   1              1            
      1550   319.00599     -9.8372065      0.0034851739   1              1            
      1600   316.48228     -15.940319      0.0034851739   1              1            
      1650   277.213        1.3856424      0.0034851739   1              1            
      1700   302.34736     -27.623644      0.0034851739   1              1            
      1750   312.06738     -52.786773      0.0034851739   1              1            
      1800   232.82457     -8.2208725      0.0034851739   1              1            
      1850   219.66312      0.0019676295   0.0034851739   1              1            
      1900   245.49515     -24.208901      0.0034851739   1              1            
      1950   262.40648     -1.8634047      0.0034851739   1              1            
      2000   307.5184       10.588572      0.0034851739   1              1            
      2050   316.54878      8.3925575      0.0034851739   1              1            
      2100   318.99324      29.042199      0.0034851739   1              1            
      2150   352.69886      18.443891      0.0034851739   1              1            
      2200   326.32556     -38.670826      0.0034851739   1              1            
      2250   333.73083      15.388091      0.0034851739   1              1            
      2300   258.51644     -42.524581      0.0034851739   1              1            
      2350   259.55019     -23.484535      0.0034851739   1              1            
      2400   289.75114      28.367986      0.0034851739   1              1            
      2450   312.34376      10.345659      0.0034851739   1              1            
      2500   298.65847     -14.077573      0.0034851739   1              1            
      2550   237.48617     -55.545493      0.0034851739   1              1            
      2600   266.79718     -17.165884      0.0034851739   1              1            
      2650   297.32794     -30.336059      0.0034851739   1              1            
      2700   258.77594     -1.3622741      0.0034851739   1              1            
      2750   240.05564     -0.4418629      0.0034851739   1              1            
      2800   189.88737     -13.20747       0.0034851739   1              1            
      2850   260.84014     -18.597276      0.0034851739   1              1            
      2900   299.99473     -7.3249394      0.0034851739   1              1            
      2950   377.90497      18.041664      0.0034851739   1              1            
      3000   263.92156     -54.260856      0.0034851739   1              1            
      3050   273.64003      26.973976      0.0034851739   1              1            
      3100   276.52232     -3.8583179      0.0034851739   1              1            
      3150   351.27802      84.899229      0.0034851739   1              1            
      3200   327.48822     -10.339189      0.0034851739   1              1            
      3250   356.11987      16.719201      0.0034851739   1              1            
      3300   263.01966     -18.033913      0.0034851739   1              1            
      3350   285.41196     -24.466282      0.0034851739   1              1            
      3400   233.65271     -39.293739      0.0034851739   1              1            
      3450   276.32895      44.300639      0.0034851739   1              1            
      3500   300.42687      28.489275      0.0034851739   1              1            
      3550   254.03142     -24.335427      0.0034851739   1              1            
      3600   304.6963       4.5827938      0.0034851739   1              1            
      3650   321.1785      -15.477109      0.0034851739   1              1            
      3700   256.00258      25.354176      0.0034851739   1              1            
      3750   356.60667     -5.4004451      0.0034851739   1              1            
      3800   361.31092     -1.481153       0.0034851739   1              1            
      3850   253.80196     -1.2120222      0.0034851739   1              1            
      3900   258.01895      19.280499      0.0034851739   1              1            
      3950   261.55352     -47.57161       0.0034851739   1              1            
      4000   254.54757     -8.6460339      0.0034851739   1              1            
      4050   301.56201      22.484551      0.0034851739   1              1            
      4100   304.73035     -31.321217      0.0034851739   1              1            
      4150   307.14343      0.5455717      0.0034851739   1              1            
      4200   291.05765      51.79974       0.0034851739   1              1            
      4250   333.73864     -24.668278      0.0034851739   1              1            
      4300   370.55562     -11.922425      0.0034851739   1              1            
      4350   408.03441      8.5963114      0.0034851739   1              1            
      4400   329.13138     -25.679871      0.0034851739   1              1            
      4450   366.98033      26.287047      0.0034851739   1              1            
      4500   311.80954      31.766893      0.0034851739   1              1            
      4550   292.28765      13.064974      0.0034851739   1              1            
      4600   320.72746     -49.078838      0.0034851739   1              1            
      4650   271.7173      -3.6846681      0.0034851739   1              1            
      4700   305.69502      37.947369      0.0034851739   1              1            
      4750   304.57521      52.411498      0.0034851739   1              1            
      4800   299.22173      12.555443      0.0034851739   1              1            
      4850   317.1756      -14.332118      0.0034851739   1              1            
      4900   330.62798      23.762097      0.0034851739   1              1            
      4950   342.34292     -21.428049      0.0034851739   1              1            
      5000   415.76656      10.136854      0.0034851739   1              1            
      5050   381.90086      18.17029       0.0034851739   1              1            
      5100   380.63709      28.042746      0.0034851739   1              1            
      5150   321.578        31.648896      0.0034851739   1              1            
      5200   301.22258     -29.246031      0.0034851739   1              1            
      5250   277.39891     -33.660526      0.0034851739   1              1            
      5300   259.34417     -47.78529       0.0034851739   1              1            
      5350   254.36079      10.616064      0.0034851739   1              1            
      5400   242.39213      29.468553      0.0034851739   1              1            
      5450   273.79403     -21.736668      0.0034851739   1              1            
      5500   367.30713     -6.0185517      0.0034851739   1              1            
      5550   309.52317      20.860119      0.0034851739   1              1            
      5600   316.82746     -10.339826      0.0034851739   1              1            
      5650   248.8707       33.659016      0.0034851739   1              1            
      5700   314.30152      19.05817       0.0034851739   1              1            
      5750   307.09966      14.458312      0.0034851739   1              1            
      5800   313.07936      15.825371      0.0034851739   1              1            
      5850   255.76382      23.890796      0.0034851739   1              1            
      5900   274.57947     -0.19520339     0.0034851739   1              1            
      5950   286.72486     -0.92397306     0.0034851739   1              1            
      6000   304.60873     -4.3983652      0.0034851739   1              1            
      6050   271.84784     -60.940602      0.0034851739   1              1            
      6100   283.48258     -8.2903551      0.0034851739   1              1            
      6150   336.07933     -8.2576526      0.0034851739   1              1            
      6200   363.09919     -17.309847      0.0034851739   1              1            
      6250   305.63822      14.475989      0.0034851739   1              1            
      6300   274.59195      49.13711       0.0034851739   1              1            
      6350   302.91015     -21.034604      0.0034851739   1              1            
      6400   293.87945      0.74647589     0.0034851739   1              1            
      6450   320.03843      47.624624      0.0034851739   1              1            
      6500   329.4551      -52.788127      0.0034851739   1              1            
      6550   320.74765      7.9598838      0.0034851739   1              1            
      6600   290.63144     -19.66089       0.0034851739   1              1            
      6650   266.9576       18.962642      0.0034851739   1              1            
      6700   274.61389     -9.823603       0.0034851739   1              1            
      6750   210.31417     -4.5767817      0.0034851739   1              1            
      6800   258.23732      44.233497      0.0034851739   1              1            
      6850   269.33119     -41.097429      0.0034851739   1              1            
      6900   318.88077     -21.601871      0.0034851739   1              1            
      6950   333.85796      26.067522      0.0034851739   1              1            
      7000   320.59631     -44.226656      0.0034851739   1              1            
      7050   348.15593      56.564077      0.0034851739   1              1            
      7100   291.30894      7.6597589      0.0034851739   1              1            
      7150   261.87574     -1.926724       0.0034851739   1              1            
      7200   318.17418      61.577301      0.0034851739   1              1            
      7250   269.73912     -41.921242      0.0034851739   1              1            
      7300   235.40776     -7.8606915      0.0034851739   1              1            
      7350   344.03017      73.910798      0.0034851739   1              1            
      7400   335.03212      13.288114      0.0034851739   1              1            
      7450   350.0822      -22.899498      0.0034851739   1              1            
      7500   360.69025     -78.556242      0.0034851739   1              1            
      7550   316.85895     -26.533434      0.0034851739   1              1            
      7600   271.65568      32.425371      0.0034851739   1              1            
      7650   264.7899      -40.230568      0.0034851739   1              1            
      7700   281.36612      8.9888402      0.0034851739   1              1            
      7750   276.96176      1.8256977      0.0034851739   1              1            
      7800   330.1516      -19.751957      0.0034851739   1              1            
      7850   325.80791     -12.52799       0.0034851739   1              1            
      7900   322.07086      35.21732       0.0034851739   1              1            
      7950   310.09493     -37.779071      0.0034851739   1              1            
      8000   309.87152      40.561377      0.0034851739   1              1            
      8050   252.91862     -27.545616      0.0034851739   1              1            
      8100   308.23471     -25.313089      0.0034851739   1              1            
      8150   278.69561      19.299388      0.0034851739   1              1            
      8200   270.81879      33.341696      0.0034851739   1              1            
      8250   312.58182      19.404863      0.0034851739   1              1            
      8300   302.20303      19.388391      0.0034851739   1              1            
      8350   299.55144     -12.952851      0.0034851739   1              1            
      8400   330.13129     -34.998178      0.0034851739   1              1            
      8450   281.66968      24.865214      0.0034851739   1              1            
      8500   262.4416       1.0196786      0.0034851739   1              1            
      8550   268.47784      44.761905      0.0034851739   1              1            
      8600   274.80898      8.6257741      0.0034851739   1              1            
      8650   264.82423     -3.9236534      0.0034851739   1              1            
      8700   268.88205      3.7102664      0.0034851739   1              1            
      8750   315.78315     -44.215318      0.0034851739   1              1            
      8800   280.19362     -4.2172962      0.0034851739   1              1            
      8850   331.88665      58.274571      0.0034851739   1              1            
      8900   314.70472      36.746006      0.0034851739   1              1            
      8950   395.82228      53.308443      0.0034851739   1              1            
      9000   351.95636      29.133084      0.0034851739   1              1            
      9050   369.74695     -37.487774      0.0034851739   1              1            
      9100   259.4453      -2.1826545      0.0034851739   1              1            
      9150   294.9952      -44.357151      0.0034851739   1              1            
      9200   273.94092      12.07438       0.0034851739   1              1            
      9250   257.18809     -29.792606      0.0034851739   1              1            
      9300   269.54343     -19.617554      0.0034851739   1              1            
      9350   301.09849     -26.979046      0.0034851739   1              1            
      9400   316.93675     -46.890327      0.0034851739   1              1            
      9450   304.52185     -8.8525101      0.0034851739   1              1            
      9500   371.73494      11.979311      0.0034851739   1              1            
      9550   291.23417      8.1900851      0.0034851739   1              1            
      9600   359.20912      38.693544      0.0034851739   1              1            
      9650   321.73443      33.448943      0.0034851739   1              1            
      9700   362.4237       36.54429       0.0034851739   1              1            
      9750   296.19875     -11.425255      0.0034851739   1              1            
      9800   329.9426       16.039783      0.0034851739   1              1            
      9850   296.79216      40.176303      0.0034851739   1              1            
      9900   345.63868      43.479483      0.0034851739   1              1            
      9950   282.27772     -49.08352       0.0034851739   1              1            
     10000   286.24393     -12.060687      0.0034851739   1              1            
Loop time of 1.29509 on 1 procs for 10000 steps with 44 atoms

Performance: 667.133 ns/day, 0.036 hours/ns, 7721.451 timesteps/s, 339.744 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.065326   | 0.065326   | 0.065326   |   0.0 |  5.04
Bond    | 0.23111    | 0.23111    | 0.23111    |   0.0 | 17.84
Kspace  | 0.94073    | 0.94073    | 0.94073    |   0.0 | 72.64
Neigh   | 0.0032599  | 0.0032599  | 0.0032599  |   0.0 |  0.25
Comm    | 0.0013719  | 0.0013719  | 0.0013719  |   0.0 |  0.11
Output  | 0.00093869 | 0.00093869 | 0.00093869 |   0.0 |  0.07
Modify  | 0.049692   | 0.049692   | 0.049692   |   0.0 |  3.84
Other   |            | 0.002667   |            |       |  0.21

Nlocal:             44 ave          44 max          44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             14 ave          14 max          14 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            869 ave         869 max         869 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 869
Ave neighs/atom = 19.75
Ave special neighs/atom = 6.4090909
Neighbor list builds = 209
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:01
